In Survive: Escape from Atlantis with the giant squid mini-expansion, the whales and squids are treated as being roughly the same critter. Does this mean that the anti-whale tiles can be used to defend against marauding squids?
Yes, you can use the anti-whale tiles to defend against the giant squid.
The Giant Squid and Whale are meant to be largely interchangeable, at least in how they are brought into and out of play. Since a player must select either a whale OR a Giant Squid, they may also choose to harpoon either by play of the defensive whale tile (but only one "harpooning" per tile, please!)